I have run into the problem where pro site users of a lower level can install and use themes that are only available to users of a higher level.
I have two levels available. "1. Essential Ministry" and "2. Complete Ministry". I have limited the themes under 'Premium Themes' within Pro Sites.
A ministry that is set to "Essential Ministry" is able to install and use themes that are set to "Complete Ministry" only. The themes are not network activated.
Themes that are set to "None" do not appear (which is what I would expect.) I checked the plugins to see if they were limiting properly and the do limit based on level as expected.
I have gone through the settings page and have updated the settings. I have done the same for the themes page. I have also checked, rechecked, and reset the ministry to make sure it is set to "Essential Ministry".
Running Wordpress 3.8